Phylogeny of the subgenus<i>Eumitria</i>in Tanzania

Temu, Stella G.; Clerc, Philippe; Tibell, Leif; Tibuhwa, Donatha Damian; Tibell, Sanja

doi:10.1080/21501203.2019.1635217

Cited by 8 publications

(48 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1 or as Usnea lineage 14A in the corresponding publication, i.e., denoting specific taxa without a formal name awaiting further work (Wirtz et al 2006;Gerlach et al 2019aGerlach et al , 2020. In three cases (MF669881, MF669883, MN080241), the full identification provided in the publication deviated from that of the GenBank accession (Gerlach et al 2019a;Temu et al 2019). For 65 accessions, the labels given in the principal components of the published work (voucher specimens, phylogenetic trees) differed from those submitted with the accessions.…”

Section: Categorymentioning

confidence: 98%

“…is one of the largest genuslevel clades of lichenized fungi, currently listed among the ten most speciose genera, with approximately 350 taxa (Thell et al 2012;Lücking et al 2017a). The classification of usneoid lichens has been in flux, besides Protousnea (Motyka) Krog either recognizing a single genus Usnea s.lat., with several subgenera and sections (Motyka 1936(Motyka , 1938Ohmura 2002;Ohmura & Kanda 2004;Wirtz et al 2006;Truong & Clerc 2013;Ohmura & Kashiwadani 2018;Temu et al 2019) or separating Dolichousnea (Y. Ohmura) Articus, Eumitria Stirt., and Neuropogon Nees & Flot. (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…Most subsequent works utilizing the ITS, without or with additional markers, focused on species taxonomy, with emphasis on neuropogonoid taxa (Seymour et al 2007;Wirtz et al 2008Wirtz et al , 2012. Several studies worked on other groups within Usnea s.lat., such as Eumitria (Temu et al 2019), Usnea s.str. with pigmented cortex (Ohmura 2008), and the U. cornuta Körb.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

View full text Add to dashboard Cite

We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.

show abstract

Section: Categorymentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

View full text Add to dashboard Cite

show abstract

“…In a detailed analysis of all available ITS barcoding data for this hyperdiverse genus (in the definition by Lücking et al 2017a), Lücking et al (2020c) demonstrated numerous shortcomings in sequence data pertaining to Usnea: first and foremost taxonomic and geographic gaps, but also substantial issues with sequence identifications and voucher information. In addition, species identification in Usnea is challenging, as many presumably widespread taxa represent complexes of partly unrelated lineages and much work remains to be done to fully resolve the taxonomy of this genus (Seymour et al 2007;Wirtz et al 2008Wirtz et al , 2012Lumbsch & Wirtz 2011;Saag et al 2011;Shen et al 2012;Truong & Clerc 2012Truong et al 2013a, b;Clerc 2016;Mark et al 2016;Gerlach et al 2017Gerlach et al , 2019Gerlach et al , 2020Clerc & Otte 2018;Grewe et al 2018;Lagostina et al 2018;Dorey et al 2019;Temu et al 2019;Lücking et al 2020c).…”

Section: Introductionmentioning

confidence: 99%

Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

Moncada¹,

Sipman²,

Lücking³

2020

Plant and Fungal Systematics

View full text Add to dashboard Cite

We tested the functionality of ITS-based DNA barcoding in lichen fungi using Colombian samples of the genus Usnea as an example. New ITS sequences were generated for 15 samples from five localities in two different ecoregions, representing varying morphologies and medullary chemistries. We employed five strategies to identify the samples: (1) BLASTn on the NCBI BLAST site with the original identifications of the best matching reference sequences; (2) as previous, but with revised identifications of the reference sequences based on a separately published revision of ITS sequences published for the genus; (3) local BLASTn in BioEdit using a separately published, revised and curated set of ITS reference sequences for the genus; (4) multiple alignment based phylogenetic analysis within the framework of all available ITS sequences for Usnea s.str.; and (5) integrative taxonomy, combining molecular phylogeny and comparative analysis of phenotype and chemical data. Using the latter approach as reference, we found that NCBI BLASTn with original identifications performed poorly, resulting in an identification success rate of only 7% (a single sample). NCBI BLASTn with revised identifications more than tripled identification success (23%), but was still unsatisfactory. Local BLASTn in BioEdit using the revised, curated reference data further doubled identification success (47%), but remained inadequate. Multiple alignment-based phylogenetic analysis achieved an identification success rate of 80% compared to the result from integrative taxonomy. Based on these results, we conclude that ITS-based DNA barcoding of the genus Usnea under the current circumstances performs poorly, but can be substantially improved using three strategies: (1) update identifications of reference sequences in primary repositories such as GenBank or alternatively use a curated reference data set; (2) perform local BLAST with a curated reference data set focusing on the target genus only, combined with multiple alignment-based phylogenetic analysis as a verification step; and (3) close substantial geographic and taxonomic gaps in the existing reference data. Our analyses suggest that if a near-complete reference data set with correct identifications existed for the genus, then standard BLAST approaches could achieve high levels of identification success close to 100%. As part of our DNA barcoding exercise, which generated the first 15 ITS sequences for Colombian samples of the genus Usnea, we confirm the presence of U. aranea and U. wasmuthii in Colombia and we report for the first time U. tenuicorticata for the country.

show abstract

“…However, he has also contributed to other topics in his active life as a researcher (Fig. 3), including: lichen conservation in Switzerland and the red-list (e.g., Vust et al 2015), lichen inventory (e.g., Habashi & Clerc 2012, 2013a, chemistry (e.g., Gadea et al 2019), molecular biology (Armaleo & Clerc 1991, 1995Döring et al 2000;Truong et al 2013;Divakar et al 2015;Gerlach et al 2018;Temu et al 2019;Jung et al 2019), the taxonomy in genera other than Usnea (e.g., Botryolepraria Canals et al, Candelariella Müll. Arg., Melanohalea O. Blanco et al, Melaspilea Nyl., Menegazzia A.…”

mentioning

confidence: 99%

A tribute to Philippe Clerc: an eminent and multitalented lichenologist in Switzerland

Gerlach¹,

Rodrigues²,

Rodríguez³

et al. 2020

Plant and Fungal Systematics

View full text Add to dashboard Cite

Phylogeny of the subgenusEumitriain Tanzania

Cited by 8 publications

References 35 publications

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

A tribute to Philippe Clerc: an eminent and multitalented lichenologist in Switzerland

Contact Info

Product

Resources

About